Co-infection with human immunodeficiency virus type 1 (HIV+) and human papillomavirus (HPV) are risk factors for anal neoplasia, but a gap exists where it is unclear what unique role HIV plays in pathogenesis. The design to recruit ?HIV magnetic (HIV sero-discordant)? couples provides an opportunity to study the unique HIV-effect in anal neoplasia. For HIV-seronegative (HIV-) men-who-have-sex-with-men (MSM), data suggest other risk factors (smoking, receptive anal sex, drug use) are associated with anal HPV infection and thus anal neoplasia. However, how HIV per se alters pathogenesis/mechanisms leading to anal neoplasia requires further study to guide screening, prognosis and treatment decisions. Addressing this gap in our knowledge responds to Provocative Question # 5 of RFA-CA-15-013 to stimulate research to delineate differences or similarities between anal neoplasia in HIV- and HIV+ patients by assessing tissue microenvironment and biomarkers. The project also responds to NIH HIV/AIDS Research Priorities and Guidelines (NOT-OD-15-137) as a High Priority research topic with HIV-associated comorbidity addressing the impact of HIV-associated malignancy and chronic HIV disease and therapy. While the relationship of high-risk HPV subtypes (hr-HPV) to anal neoplasia is known, a proliferation marker, p16, may also play a role since HPV E7 protein binding results in p16 expression. HIV tat protein enhances E2-dependent HPV transcription which may enhance HIV/HPV- mediated cancers. Neoplastic squamous epithelial cells also display unique Raman spectra, a technique to identify cellular chemical molecules by laser scatter, which could influence microenvironments. By exploring a biomarker dyad (hr-HPV, p16) in anal cytologies, we will attest if anal HIV DNA discriminates squamous cell carcinoma (SCC), high-grade- or low-grade squamous intraepithelial lesions (HSIL, LSIL). Anal neoplastic cells will be compared for Raman spectra differences or similarities to assess cellular microenvironments. Our central hypotheses are that HIV DNA will influence anal biomarker dyad to discriminate anal neoplasia of HIV+ individuals from HIV- partners; and the Raman spectra of anal neoplastic cells from HIV+ individuals will be distinct from HIV- individuals. The proposal is innovative by assessing biomarker dyad with Raman spectroscopy to determine the HIV-effect in HIV magnetic couples. The significance lies in understanding how anal HIV DNA influences the biomarker dyad and identifying the Raman spectra microenvironment thus contributing to our understanding of pathogenesis of HPV anal neoplasia in HIV+ patients. The transdisciplinary team has pioneered work on biomarkers and Raman spectroscopy to be well-positioned for the project. By recruiting 25 HIV- and HIV+ MSM couples, we propose: 1) To determine if a biomarker dyad (hr-HPV, p16) is influenced by HIV DNA copy number in anal cytologies and anal biopsies from HIV magnetic couples; 2) To define the Raman spectra fingerprint of anal neoplastic cells obtained from biopsies from HIV magnetic couples; and 3) To determine risk factors from HIV magnetic couples for anal neoplasia.